The influence of vacancies in the C sublattice of MgCNi3, on its structural, electronic, and magnetic properties are studied by means of the density-functional-based Korringa-Kohn-Rostoker Green's function method formulated in the atomic sphere approximation. Disorder is taken into account by means of coherent-potential approximation. Characterizations representing the change in the lattice properties include the variation in the equilibrium lattice constants, bulk modulus, and pressure derivative of the bulk modulus, and those of the electronic structure include the changes in the total, partial, and k-resolved density of states. The incipient magnetic properties are studied by means of the fixed-spin moment method of alloy theory, together in conjunction with the phenomenological Ginzburg-Landau equation for magnetic phase transition. The first-principles calculations reveal that due to the breaking of the C-Ni bonds, some of the Ni 3d states, which were lowered in energy due to strong hybridization, are transferred back to higher energies thereby increasing the itinerant character in the material. The Bloch spectral densities evaluated at the high symmetry points, however, reveal that the charge redistribution is not uniform over the cubic Brillouin zone, as new states are seen to be created at the Gamma point, while a shift in the states on the energy scale are seen at other high symmetry points.